Journal ArticleDOI
Microarray data normalization and transformation
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TLDR
This review focuses on the much more mundane but indispensable tasks of 'normalizing' data from individual hybridizations to make meaningful comparisons of expression levels, and of 'transforming' them to select genes for further analysis and data mining.Abstract:
Underlying every microarray experiment is an experimental question that one would like to address. Finding a useful and satisfactory answer relies on careful experimental design and the use of a variety of data-mining tools to explore the relationships between genes or reveal patterns of expression. While other sections of this issue deal with these lofty issues, this review focuses on the much more mundane but indispensable tasks of 'normalizing' data from individual hybridizations to make meaningful comparisons of expression levels, and of 'transforming' them to select genes for further analysis and data mining.read more
Citations
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The analysis of Lupinus albus root proteome revealed cytoskeleton altered features due to long-term boron deficiency.
TL;DR: The adaptive responses of Lupinus albus roots to long-term B deficiency are analyzed, and detected changes in cytoskeletal associated proteins indicate altered cytOSkeletal biosynthesis and suggest that B may have an important contribution in this process.
Journal ArticleDOI
Improved production of secreted heterologous enzyme in Bacillus subtilis strain MGB874 via modification of glutamate metabolism and growth conditions
Kenji Manabe,Yasushi Kageyama,Takuya Morimoto,Eri Shimizu,Hiroki Takahashi,Shigehiko Kanaya,Katsutoshi Ara,Katsuya Ozaki,Naotake Ogasawara +8 more
TL;DR: High levels of production of alkaline cellulase Egl-237 are found with the reduced-genome strain 874∆rocG and using the NH3-pH auxostat fermentation, possibly due to improved glutamate synthesis and enhanced generation of metabolism energy.
Journal ArticleDOI
Opa Interacting Protein 5 (OIP5) Is a Novel Cancer-testis Specific Gene in Gastric Cancer
Yoshito Nakamura,Fumiaki Tanaka,Hisashi Nagahara,Keisuke Ieta,Naotsugu Haraguchi,Koshi Mimori,Atsushi Sasaki,Hiroshi Inoue,Katsuhiko Yanaga,Masaki Mori +9 more
TL;DR: Using a combination of LMD and microarray, OIP5 was identified as a cancer-testis specific gene and may be a novel immunotherapy target for patients with gastric cancer.
Journal ArticleDOI
The 'yeast cell wall chip' - a tool to analyse the regulation of cell wall biogenesis in Saccharomyces cerevisiae.
José Manuel Rodríguez-Peña,R. Pérez-Diaz,Sara Alvarez,Clara Bermejo,Raúl García,Catalina Santiago,César Nombela,Javier Arroyo +7 more
TL;DR: The design and production of a gene microarray, called the 'yeast cell wall chip', specifically tailored to investigate cell wall functions, is described, which has been validated and shown to be useful to address gene involvement in the regulation of the response to cell wall damage in yeast.
Journal ArticleDOI
A global analysis of adaptive evolution of operons in cyanobacteria.
TL;DR: The results suggest that while in situ formation and vertical descent may be a dominant mechanism of operon evolution in cyanobacteria, optimization of intergenic spacing and co-regulation are part of an ongoing process in the life-cycle of operons.
References
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Journal ArticleDOI
Cluster analysis and display of genome-wide expression patterns
TL;DR: A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression, finding in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function.
Book
Data Reduction and Error Analysis for the Physical Sciences
TL;DR: In this paper, Monte Carlo techniques are used to fit dependent and independent variables least squares fit to a polynomial least-squares fit to an arbitrary function fitting composite peaks direct application of the maximum likelihood.
Journal ArticleDOI
Data Reduction and Error Analysis for the Physical Sciences.
TL;DR: Numerical methods matrices graphs and tables histograms and graphs computer routines in Pascal and Monte Carlo techniques dependent and independent variables least-squares fit to a polynomial least-square fit to an arbitrary function fitting composite peaks direct application of the maximum likelihood.
Journal ArticleDOI
Robust Locally Weighted Regression and Smoothing Scatterplots
TL;DR: Robust locally weighted regression as discussed by the authors is a method for smoothing a scatterplot, in which the fitted value at z k is the value of a polynomial fit to the data using weighted least squares, where the weight for (x i, y i ) is large if x i is close to x k and small if it is not.
Book
Regression Analysis by Example
Samprit Chatterjee,B. Price +1 more
TL;DR: Simple linear regression Multiple linear regression Regression Diagnostics: Detection of Model Violations Qualitative Variables as Predictors Transformation of Variables Weighted Least Squares The Problem of Correlated Errors Analysis of Collinear Data Biased Estimation of Regression Coefficients Variable Selection Procedures Logistic Regression Appendix References as discussed by the authors